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FF:1271-21F2

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Name:spleen, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11011
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuespleen
dev stage18 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004920
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11011 CAGE DRX009086 DRR009960
Accession ID Mm9

Library idBAMCTSS
CNhs11011 DRZ001385 DRZ002768
Accession ID Mm10

Library idBAMCTSS
CNhs11011 DRZ012735 DRZ014118
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data

CNhs11011

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0573
1001 0
1002 0.254
1003 --0.0842
1004 0
1005 0.223
1006 --0.143
1007 --0.0247
1008 0
1009 0.0508
101 0.152
1010 0
1011 --0.0131
1012 0.0738
1013 --0.0799
1014 0.192
1015 --0.00719
1016 --0.00909
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0738
1022 --0.246
1023 0.0738
1024 0.102
1025 0.192
1026 0
1027 0
1028 0
1029 0.142
103 0.0738
1030 0.192
1031 0.201
1032 --0.147
1033 0.0738
1034 0.0506
1035 0
1036 0.297
1037 0
1038 --0.102
1039 --0.211
104 0
1040 0.176
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11011

Jaspar motif P-value
MA0002.2 0.00172
MA0003.1 0.458
MA0004.1 0.83
MA0006.1 0.137
MA0007.1 0.658
MA0009.1 0.231
MA0014.1 0.967
MA0017.1 0.921
MA0018.2 2.51421e-7
MA0019.1 0.604
MA0024.1 6.05905e-7
MA0025.1 0.0017
MA0027.1 0.147
MA0028.1 0.0331
MA0029.1 0.808
MA0030.1 0.261
MA0031.1 0.414
MA0035.2 1.0515e-5
MA0038.1 0.429
MA0039.2 0.277
MA0040.1 0.921
MA0041.1 0.191
MA0042.1 0.542
MA0043.1 0.0103
MA0046.1 3.32153e-10
MA0047.2 0.898
MA0048.1 0.0174
MA0050.1 1.02382e-7
MA0051.1 4.73432e-5
MA0052.1 1.316e-5
MA0055.1 0.0223
MA0057.1 0.775
MA0058.1 0.906
MA0059.1 0.64
MA0060.1 0.606
MA0061.1 0.00334
MA0062.2 8.21893e-6
MA0065.2 0.766
MA0066.1 0.6
MA0067.1 0.155
MA0068.1 0.955
MA0069.1 0.366
MA0070.1 0.261
MA0071.1 0.43
MA0072.1 0.343
MA0073.1 0.879
MA0074.1 0.739
MA0076.1 0.0289
MA0077.1 0.271
MA0078.1 0.368
MA0079.2 0.139
MA0080.2 1.052e-13
MA0081.1 9.32232e-4
MA0083.1 0.967
MA0084.1 0.96
MA0087.1 0.0725
MA0088.1 0.14
MA0090.1 0.157
MA0091.1 0.207
MA0092.1 0.669
MA0093.1 0.848
MA0099.2 0.448
MA0100.1 0.848
MA0101.1 0.0321
MA0102.2 0.0195
MA0103.1 0.00141
MA0104.2 0.63
MA0105.1 1.11841e-5
MA0106.1 0.783
MA0107.1 0.0367
MA0108.2 0.144
MA0111.1 0.847
MA0112.2 0.0159
MA0113.1 0.385
MA0114.1 0.167
MA0115.1 0.033
MA0116.1 0.00403
MA0117.1 0.418
MA0119.1 0.0831
MA0122.1 0.57
MA0124.1 0.362
MA0125.1 0.0597
MA0131.1 0.99
MA0135.1 0.101
MA0136.1 5.80958e-14
MA0137.2 0.0453
MA0138.2 0.00354
MA0139.1 0.157
MA0140.1 1.73618e-30
MA0141.1 0.522
MA0142.1 0.408
MA0143.1 0.216
MA0144.1 0.24
MA0145.1 0.939
MA0146.1 0.271
MA0147.1 0.746
MA0148.1 0.694
MA0149.1 0.612
MA0150.1 0.118
MA0152.1 0.136
MA0153.1 9.01108e-7
MA0154.1 0.00188
MA0155.1 0.65
MA0156.1 5.98618e-19
MA0157.1 0.646
MA0159.1 0.753
MA0160.1 0.404
MA0162.1 0.308
MA0163.1 1.20397e-5
MA0164.1 0.987
MA0258.1 0.341
MA0259.1 0.91



FANTOM5 phase1 novel unique motifsSummary:Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11011

Novel motif P-value
1 0.217
10 0.0466
100 0.995
101 0.662
102 0.412
103 0.0439
104 0.992
105 0.591
106 0.0614
107 0.0988
108 0.599
109 0.0566
11 0.172
110 0.132
111 0.307
112 0.0275
113 0.494
114 0.847
115 0.488
116 0.844
117 0.0104
118 0.241
119 0.509
12 0.557
120 0.806
121 0.547
122 0.724
123 0.0165
124 0.79
125 0.0955
126 0.232
127 0.354
128 0.0883
129 0.619
13 0.001
130 0.0594
131 0.948
132 0.358
133 0.144
134 0.188
135 0.441
136 0.9
137 0.0233
138 0.289
139 0.945
14 0.865
140 0.0684
141 0.911
142 0.181
143 0.255
144 0.222
145 0.00181
146 0.907
147 0.605
148 0.0296
149 0.992
15 0.0825
150 0.0687
151 0.345
152 0.701
153 0.319
154 0.714
155 0.184
156 2.71243e-20
157 0.63
158 0.142
159 0.186
160 0.0616
161 0.0798
162 0.645
163 0.782
164 0.00798
165 0.124
166 0.778
167 0.436
168 0.848
169 0.0277
17 0.658
18 0.47
19 0.19
2 0.648
20 0.271
21 0.183
22 0.46
23 0.721
24 0.175
25 0.91
26 0.00303
27 0.987
28 0.681
29 0.0526
3 0.0215
30 0.631
31 0.977
32 0.961
33 0.13
34 0.516
35 0.697
36 0.316
37 0.109
38 0.757
39 0.694
4 0.695
40 0.25
41 0.609
42 0.0259
43 0.0986
44 0.354
45 0.903
46 0.11
47 0.423
48 0.304
49 0.209
5 0.17
50 0.223
51 0.969
52 0.771
53 0.666
54 0.791
55 0.251
56 0.56
57 0.0995
58 0.56
59 0.128
6 0.725
60 0.144
61 0.104
62 0.287
63 0.381
64 0.552
65 0.928
66 0.827
67 0.158
68 0.625
69 0.984
7 0.0106
70 0.751
71 0.00856
72 0.31
73 0.28
74 0.361
75 0.176
76 0.652
77 0.984
78 0.0131
79 0.443
8 0.0884
80 0.00974
81 0.614
82 0.364
83 0.917
84 0.00255
85 0.807
86 0.873
87 0.0476
88 0.808
89 0.981
9 0.293
90 0.17
91 0.151
92 0.569
93 0.411
94 0.161
95 0.207
96 0.416
97 0.938
98 0.362
99 0.414



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs11011


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002106 (spleen)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002323 (body cavity)
0005177 (trunk region element)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000302 (mouse embryonic day 18 sample)
0011517 (mouse spleen-, embryo E18 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)